The novitiate phase is the extended time of reflection and experience that marks the woman's formal beginning of religious life in the congregation. The novitiate is the first prolonged experience of reflecting on oneself, God, the Church, and the congregation of the Sisters of St. Joseph of the Third Order of St. Francis. The novitiate phase usually consists of two years. The first year is the canonical year and the second is the apostolic year.

During the canonical year, the novice learns the essentials of religious life and what it means to live the evangelical counsels of poverty, chastity, and obedience. She studies the Franciscan documents, vows, community life, and the congregation's documents.

The focus of the apostolic year is the integration of Franciscan spirituality, communal life, and ministry. During this time, the novice prepares for her future life in the congregation. With assistance, she learns to balance her apostolic activity with the Franciscan contemplative way of life. At the completion of these two years of study, prayer, and preparation for vows, the novice moves to the next phase.